Special Issue "Structure Formation and Dynamics of Semiflexible Macromolecules"

A special issue of Polymers (ISSN 2073-4360). This special issue belongs to the section "Polymer Theory and Simulation".

Deadline for manuscript submissions: 31 May 2020.

Special Issue Editor

Dr. Arash Nikoubashman
E-Mail Website
Guest Editor
Johannes Gutenberg Universität Mainz, Staudingerweg 9 55128 Mainz, Germany
Interests: microfluidics of complex liquids; directed assembly of soft matter; semiflexible macromolecules in confinement; soft matter; chemical engineering; simulations

Special Issue Information

Dear Colleagues,

Semiflexible polymers are ubiquitous as constituents of biological matter and also find widespread use as building blocks of advanced materials. Yet, their static and dynamic behaviors are only partially understood and pose challenging questions in the context of polymer physics. Semiflexible polymers are characterized by several crossover length scales, such as the persistence and contour length, which introduce a large number of disparate time and length scales that are relevant to describing their structure formation and dynamics. In the past decade, progress in experimental and computational techniques has led to a renaissance of this research field, resulting in the verification of previous theories and the discovery of novel physical properties.

This Special Issue of Polymers is intended to cover these new advances on the structure formation and dynamics of semfilexible macromolecules from experiments, simulations, and theory. Various synthetic and natural macromolecules are of interest, which may be linear, cyclic, star-like or of any other topology. The systems can be in melt or in solution, in equilibrium or under nonequilibrium conditions, e.g., under flow, in confinement, or with activity. Preferably, contributions shall focus on the emergence of mesoscopic/macroscopic ordering, e.g., nematic or smectic, originating from the intrinsic stiffness of the macromolecules. Both original contributions and brief reviews are welcome.

Dr. Arash Nikoubashman
Guest Editor

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All papers will be peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Polymers is an international peer-reviewed open access monthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 1500 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • Semiflexible polymers
  • Biopolymers
  • Persistence length
  • Nematic/smectic/cholesteric ordering
  • Self-assembly
  • Topological defects
  • Experiments
  • Simulations
  • Theory

Published Papers (1 paper)

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Research

Open AccessArticle
Entropy-induced Separation of Binary Semiflexible Ring Polymer Mixtures in Spherical Confinement
Polymers 2019, 11(12), 1992; https://doi.org/10.3390/polym11121992 - 02 Dec 2019
Abstract
Coarse-grained molecular dynamics simulations are used to investigate the conformations of binary semiflexible ring polymers (SRPs) of two different lengths confined in a hard sphere. Segregated structures of SRPs in binary mixtures are strongly dependent upon the number density of system (ρ [...] Read more.
Coarse-grained molecular dynamics simulations are used to investigate the conformations of binary semiflexible ring polymers (SRPs) of two different lengths confined in a hard sphere. Segregated structures of SRPs in binary mixtures are strongly dependent upon the number density of system (ρ), the bending energy of long SRPs (Kb, long), and the chain length ratio of long to short SRPs (α). With a low ρ or a weak Kb, long at a small ratio α, long SRPs are immersed randomly in the matrix of short SRPs. As ρ and bending energy of long SRPs (Kb, long) are increased up to a certain value for a large ratio α, a nearly complete segregation between long and short SRPs is observed, which can be further characterized by the ratio of tangential and radial components of long SRPs velocity. These explicit segregated structures of the two components in spherical confinement are induced by a delicate competition between the entropic excluded volume (depletion) effects and bending contributions. Full article
(This article belongs to the Special Issue Structure Formation and Dynamics of Semiflexible Macromolecules)
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Planned Papers

The below list represents only planned manuscripts. Some of these manuscripts have not been received by the Editorial Office yet. Papers submitted to MDPI journals are subject to peer-review.

Title: Performance of coarse graining in estimating polymer properties: comparison with the atomistic model
Author: Noriyoshi Arai
Abstract: Combining atomistic and coarse-grained (CG) models is a promising approach for quantitative prediction of polymer properties. However, the gaps between the length and time scales of atomistic and CG models still need to be bridged. Here, the scale gaps of the atomistic model of polyethylene melts, bead–spring Kremer–Grest model, and dissipative particle dynamics with the slip-spring model were investigated. A single set of spatial and temporal scaling factors was determined between the atomistic model and each CG model. The results of the CG models were rescaled using the set of scaling factors and compared with those of the atomistic model. For each polymer property, a threshold value indicating the onset of static or dynamic universality of polymers was obtained.

Title: Non-equilibrium overstretching and intercalation of dsDNA
Authors: Maarten Sebregts, Andreas Biebricher, Erwin Peterman, Gijs Wuite, Iddo Heller, Paul van
der Schoot and Cornelis Storm
Abstract: Double-stranded DNA subject to a steadily increasing tension undergoes an overstretching
transition at about 70 pN stretching force [1]. The native, helical ground state then unwinds to an
overstretched, nearly unwound state that is 70% longer. Intercalating fluorescent dye molecules, often
used for visualisation purposes, greatly affect this transition. Both the overstretching and the binding
and unbinding of intercalators with increasing stretching force can be described almost quantitatively
using a multi-state Kuhn model [2], at least if the stretching is sufficiently slow. If not sufficiently slow,
a different behaviour is observed not captured by the equilibrium model [3]. We build on the
equilibrium model, making use of a combination of molecular dynamics with kinetic Monte Carlo
simulation, to study the impact of intercalator binding kinetics on the mechanical properties of DNA.
Our simulations reproduce experimental force-extension curves and kymographs. At constant
intercalator concentration, we find universal behaviour for identical ratios of the stretching velocity
and intercalation rate.
References:
[1] C. Bustamante, Z. Bryant, and S. B. Smith, Ten years of tension: single-molecule DNA mechanics,
Nature, 421 (2003), 423.
[2] K. Schakenraad, A. S. Biebricher, M. Sebregts, B. ten Bensel, E. J. G. Peterman, G. J. L. Wuite, I.
Heller, C. Storm and P. van der Schoot, Hyperstretching DNA, Nat. Comm. 8 (2017), 2197.
[3] A. S. Biebricher, I. Heller, R. F. H. Roijmans, T. P. Hoekstra, E. J. G. Peterman, and G. J. L. Wuite, The
impact of DNA intercalators on DNA and DNA-processing enzymes elucidated through force-dependent
binding kinetics, Nat. Comm., 6, Jun 2015

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